Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ctcf

Cell type

Cell type Class
Neural
Cell type
Neural progenitor cells
NA
NA

Attributes by original data submitter

Sample

source_name
NPCs
chip antibody
CTCF (CST 3418)
cell type
NPCs
geo_loc_name
missing
collection_date
missing

Sequenced DNA Library

library_name
GSM7054961
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, cultured cells were fixed in 1% formaldehyde and snap frozen in liquid nitrogen and stored at -80 C for at least overnight. Sonication of tumor specimens and cultured cells was calibrated such that DNA was sheared to between 400bp and 2000bp. CTCF was immunoprecipitated with a monoclonal rabbit CTCF antibody, clone D31H2 (Cell Signaling 3418). H3K27ac was immunoprecipitated with an antibody from Active Motif (cat 39133). ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3' A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.

Sequencing Platform

instrument_model
NextSeq 550

mm10

Number of total reads
33871907
Reads aligned (%)
98.1
Duplicates removed (%)
19.4
Number of peaks
73299 (qval < 1E-05)

mm9

Number of total reads
33871907
Reads aligned (%)
97.9
Duplicates removed (%)
19.6
Number of peaks
73235 (qval < 1E-05)

Base call quality data from DBCLS SRA